GSK MMP node?

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1

Hi,

I noticed that the GSK mmp code is now available for RDKit, are there any plans to release this as a knime node?

Many thanks,

Angus

 

2

There is a MMP node using rdkit available as a knime node which was released by the erlwood UK Eli Lilly computational group. See the page at http://tech.knime.org/community/erlwood. This was programmed by George Papadatos.

there is more info here too; http://rdkit.org/UGM/2012/Evans_Papadatos_RDKit_UGM.pdf

Hope this helps,

simon.

3

Hi Simon,

Thanks for your reply, I use the erlwood node regularly and find it really useful.  The reason I asked about the GSK mmp node is that I understood it did multiple cuts to identify linkers and scaffolds also, which I think would be a useful addition.

Angus

 

4

Hi Angus, I agree multiple cuts would be useful, as you say to do mmp's on scaffold cores. It's something we've discussed in-house. If this code is already available for rdkit as open source, as you say, it would be great if someone could take this on to generate an rdkit knime node for it.

simon.

5

It's a nice method and I'd love to do it, but there is a technical hurdle to doing so (explained below), so it's probably not going to be a fast process.

The technical hurdle: the MMP code that Jameed Hussain contributed is written in Python. In order for us to make it available in Knime, we need to rewrite it in either Java or C++. I haven't read through Jameed's code in detail to see how much effort that would be, but it's not a small amount.

-greg

 

6

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